DEFA6

defensin alpha 6, the group of Defensins, alpha

Basic information

Region (hg38): 8:6924696-6926076

Links

ENSG00000164822 ∙ NCBI:1671 ∙ OMIM:600471 ∙ HGNC:2765 ∙ Uniprot:Q01524 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DEFA6 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEFA6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3		1	4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	1

Variants in DEFA6

This is a list of pathogenic ClinVar variants found in the DEFA6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-6924870-G-T		not specified	Uncertain significance (Sep 21, 2023)
8-6924877-C-G		not specified	Uncertain significance (Dec 15, 2022)
8-6925855-G-C		not specified	Uncertain significance (Oct 12, 2022)
8-6925867-C-T		not specified	Uncertain significance (Aug 12, 2021)
8-6925885-C-T		not specified	Likely benign (Dec 28, 2023)
8-6925916-C-A		not specified	Uncertain significance (Oct 17, 2023)
8-6925931-C-G			Benign (Jun 25, 2018)
8-6925972-G-A		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEFA6	protein_coding	protein_coding	ENST00000297436	2	1384

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000425	0.0670	125666	0	6	125672	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.86	89	51.5	1.73	0.00000252	636
Missense in Polyphen		31	17.115	1.8113		228
Synonymous	-3.08	38	20.3	1.87	9.96e-7	199
Loss of Function	-2.41	6	2.17	2.77	9.21e-8	26

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000440
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has very low antimicrobial activity against Gram- negative and Gram-positive bacteria. May protect cells against infection with HIV-1. {ECO:0000269|PubMed:15616305, ECO:0000269|PubMed:17088326}.
• Pathway: Antimicrobial peptides;Innate Immune System;Immune System;Alpha-defensins;Defensins (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.578
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.48

Haploinsufficiency Scores

• pHI: 0.552
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0591

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Def6
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; cellular phenotype; hematopoietic system phenotype; skeleton phenotype

Gene ontology

• Biological process: innate immune response in mucosa;antimicrobial humoral response;antibacterial humoral response;killing of cells of other organism;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;defense response to fungus;membrane disruption in other organism;antimicrobial humoral immune response mediated by antimicrobial peptide;cellular response to lipopolysaccharide
• Cellular component: extracellular region;extracellular space;Golgi lumen
• Molecular function: protein binding;protein homodimerization activity